One of the common challenges in molecular modeling is presenting protein-ligand interactions in a way that’s both visually engaging and scientifically meaningful. You might find yourself struggling to explain how a ligand fits into a binding site — or more importantly, how it comes out.
That’s where the Undock animation in SAMSON can be especially helpful. By creating an animated transition that visually ‘pulls’ atoms or meshes away from their docked positions, the Undock animation provides a clear and intuitive way to demonstrate molecular exit pathways or simply to reverse the docking process.
What is the Undock Animation?
The Undock animation in SAMSON automatically calculates a trajectory that retracts selected atoms or meshes from their current position, which is considered a docked pose. This animation is particularly effective for educational content, presentations, and mechanistic analyses of binding and unbinding events.
When Could You Use It?
- To explain the geometry of a binding site by showing how ligands exit it
- To visualize post-docking results obtained from simulations or screening methods
- To prepare animations for publications or presentations
- To test hypothetical binding/unbinding routes
How to Add the Undock Animation
1. In your SAMSON document, select at least two nodes: the receptor and one or more ligands or structures to undock.
2. The first node in your selection will be treated as the static receptor. If you need multiple nodes to act as the receptor, place them in a folder and select that folder first.
3. Then, double-click the Undock animation in the Animation panel in the Animator.
The animation will automatically calculate a movement away from the docking position between the current keyframes. You can reposition the keyframes as needed.
Customizing the Movement
The initial amplitude of the undocking motion is computed when the animation is created, but it doesn’t have to stay that way.
You can adjust the amplitude and other parameters using the Inspector panel. Additionally, if you want to control how the motion proceeds between keyframes — e.g., add an ease-in or ease-out effect — you can modify the Easing curve.
Example in Action
In this animation, the ligand is pulled away from its binding site, clearly illustrating both the shape of the binding tunnel and the ligand’s relative orientation during exit.
Tips
- If no nodes are selected when you add the animation, SAMSON will try to guess what atoms or nodes to undock. However, explicit selection is usually more precise.
- You can always move and adjust the keyframes to better fit your desired timing.
- Looking to reverse the process? Try the Dock animation instead.
To learn more about how to use the Undock animation in SAMSON, including technical details and related tools, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.